Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F2 I76 R1	7	11.0	663162	95.7%	634646	85.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,650,516	T→C	G54G (GGT→GGC)	hdeD →	acid‑resistance protein HdeD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,650,516	0	T	C	100.0%	19.5 / NA	8	G54G (GGT→GGC)	hdeD	acid‑resistance protein HdeD
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (3/5); total (3/5)

GTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGTGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATC  >  NZ_CP009273/3650429‑3650596

gTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGgcgc                                                                                <  2:200205/90‑1 (MQ=255)

          gTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGgcgc                                                                                >  1:105691/1‑80 (MQ=255)

          gTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGgcgc                                                                                <  2:105691/80‑1 (MQ=255)

                 tgTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATc                                                                      <  1:108315/83‑1 (MQ=255)

                 tgTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATc                                                                      >  2:108315/1‑83 (MQ=255)

                       tcgtcgGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTg                                                         >  1:115367/1‑90 (MQ=255)

                           cgGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCt                                                     <  2:291204/90‑1 (MQ=255)

                                              ttCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGc                                  >  1:314661/1‑90 (MQ=255)

                                                                gATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTc                <  2:209502/90‑1 (MQ=255)

                                                                       tAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGGGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCgg         <  2:314661/90‑1 (MQ=255)

                                                                              agtagtGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATc  <  2:309844/90‑1 (MQ=255)

GTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGTGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATC  >  NZ_CP009273/3650429‑3650596

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGTGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATCCGGTTT  >  NZ_CP009273/3650429‑3650602

GTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATC                                                                            >  SRR3722214.107359/1‑100 (MQ=60)

          GTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTA                                                                  <  SRR3722214.110021/100‑1 (MQ=60)

           caccgagatctacacaaggagtatcgtcggcagcgtcagatgtgtataagagacagATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTAT                                                                 <  SRR3722214.285911/44‑1 (MQ=60)

             CTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTG                                                               >  SRR3722214.117187/1‑100 (MQ=60)

                                    GTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGC                                        >  SRR3722214.320696/1‑100 (MQ=60)

                                                                          GCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATCCGGTTT  >  SRR3722214.38847/1‑100 (MQ=60)

GTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGTGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATCCGGTTT  >  NZ_CP009273/3650429‑3650602

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`